[maker-devel] Error from a malformed gff file

[Esther]

Hi,

I'm interested in re-annotating gene models with new evidence using
MAKER in a first generation genome (budding yeast). I have been able
to run it fine in de novo and reference mode as described by Holt and
Yandell in the Maize example in their 2011 BMC Bioinformatics paper
but I'm having troubles running in re-annotation mode using a gff file
with the model_gff parameter. The gff file I'm using is from SGD
(http://downloads.yeastgenome.org/curation/chromosomal_feature/
saccharomyces_cerevisiae.gff) which should be GFF3 compliant according
to this validator: https://github.com/solgenomics/gff3_validator. I
get an error due to a malformed gff file, but without knowledge of
which line(s) are offending, it's hard for me to fix the problem. Is
there a way to find that information?

The error message I get is as follows:

Making transcripts
Processing transcripts into genes
Calculating annotation quality statistics
ERROR: The feature being compared appears to be missing
some of it's structure.  This can happen when you use
a malformed GFF3 file as input to one of MAKER's evidence
passthrough options. Failed on maker-chrIII-pred_gff_blastx-
gene-0.1018-mRNA-1
(from shadow_AED::get_AED)

Thanks,
Esther